In 2001, a Proposition 2½ override failed to pass. The result was fees were implemented. Fees of $125 were implemented for music, which subsequently decimated the Barnstable High School Marching Band. Bus fees were added, which totaled around $175 and sports fees were set at $125. The music fee was later rescinded in the 2005–2006 school year.

In 2001, the school committee was sued under the court case Fitzgerald v. Barnstable School Committee. The case went all the way to the U.S. Supreme Court, which ruled that parents could sue school committees for sexual harassment under the Fourteenth Amendment. The 3 million dollar suit was eventually settled for $150,000.

With the Late-2000s recession, the state was forced to cut $6 million in local aid. Faced with this, the town took drastic measures. Option 3, which entailed closing two elementary schools, moving 4th Graders into the Horace Mann Charter School, moving 6th Graders into the Middle School, and 8th Graders into the High School. The schools that might close are Hyannis East Elementary School, Marstons Mills and Cotuit Elementary School, and Barnstable-West Barnstable Elementary School. All those schools are the oldest in the district, and are suffering from disrepair.